Noble metal oxides such as ruthenium dioxide are highly active electrocatalysts for anodic reactions in acidic electrolytes, but dissolution during electrochemical operation impedes wide-scale applications in renewable energy technologies. Improving the fundamental understanding of the dissolution dynamics of application-relevant morphologies such as nanocrystals is critical for the gridscale implementation of these materials. Herein, we report the nanoscale heterogeneity observed via liquid-phase transmission electron microscopy during ruthenium dioxide nanocrystal dissolution under oxidizing conditions. Single-crystalline ruthenium dioxide nanocrystals enabled the direct observation of dissolution along different crystallographic facets, allowing an unprecedented direct comparison of crystal facet stability. The nanoscale observations revealed substantial heterogeneity in the relative stability of crystallographic facets across different nanocrystals, attributed to the nanoscale strains present in these crystals. These findings highlight the importance of nanoscale heterogeneity in determining macroscale properties such as electrocatalyst stability and provide a characterization methodology that can be integrated into next-generation electrocatalyst discovery efforts.